If you have dedicated entire FS to use as MySQL datadir then MySQL will interpret all files under that directory as db-related files.
SHOW DATABASES lists database lost+found which is not real database.

If you check error log you can notice this message:

[ERROR] Invalid (old?) table or database name 'lost+found'

For a single server configuration issues with lost+found directory can only make confusion. I’m not aware of any negative effects for database.
To avoid confusion you should move database to sub-directory below the root level directory. Also remove all directories that are not MySql db-related from datadir location.

To avoid this inconveniences just move databases from root directory.
Some of you will simply delete lost+found directory, but be aware, fsck may recreate lost+found directory and your cluster synchronisation will fail when you least expect it ;)

Confusion and problems with lost+found directory in MySQL/Galera cluster configuration